Ghosts That We Knew
by Ballykissangel
Summary: The Doctor comes to live a normal life as John's flat mate after the death of Sherlock. John is not doing well and just wants to be alone to fade away and the Doctor tries to keep a promise as they struggle to learn to live with each other and themselves. A collection of humor, angst and tears between both Doctors as they learn things. No slash, just epic friendship. AU Wholock.
1. He Came In Quiet With The Rain

_A/N: This will be a collection of stories about The Doctor coming to live a normal life as John's flat mate after Sherlock's death. It is set a couple of months before the start of _**_When Evening Falls So _****_Hard._**

_It's based a few years after **The Angels Take Manhattan** and it will mostly be a series of angst/hurt and comfort one shots, with a little bit of humor mixed in, as both Doctors learn things they have forgotten and help each other through their dark times._

_Warning: No slash, but of a lot of tears and angst from both Doctors, so a tissue warning may apply._

_~Thank you Vintage Tea Party and Chestry007 for all your lovely help on this chapter~_

_Disclaimer: I do not own Sherlock or DW, I'm just visiting around with them._

_Cover created by Allison Rose_

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When he opened his eyes that morning, the familiar shades of gray greeted him, the gray ceiling, the gray undecorated walls of his bedroom. Through the window the presence of gray clouds threatened oncoming rain for the gray September morning and the wind was softly blowing through the trees that were starting to lose their golden brown leaves.

He forced himself to get out of bed and put his feet on the floor, everything he did now seemed to hurt even more these days since Sherlock's death and as the months passed it felt like his spirit was also passing and he dreaded when he had to get up and get himself moving.

Still in his tee-shirt and pyjama bottoms, he made himself walk to the bathroom and wash away the sweat left behind from the nightmares that had come to him in the night. He splashed water on his face, ignoring the tired and washed out blue eyes that stared back at him in the hollowed and pale face in the mirror's reflection.

The stillness and silence of his flat greeted him and reminded him of yet another day he had to face alone, but John had grown used to it and it felt it was a part of him that he accepted without question, not that he didn't have any questions for it, he was just too tired to ask them anymore.

He walked into the tiny kitchen area to make himself some tea and attempt to eat something. A few minutes later, as he sat at the bare kitchen table with his tea and an untouched piece of toast, he pulled out yesterday's newspaper and saw the ad he had reluctantly agreed to have published for a flat mate.

He had done it unwillingly of course, finally giving in under Mycroft's firm threat of either getting a flat mate to live with him or to have John taken and treated under observation for his disinterest in life whether he wanted to or not. Mycroft's reasoning was that if John had a flat mate, it would help him at least to keep moving on with his life even though he was just pretending.

He had done fairly well as to be expected the few months after the funeral, but it seemed the harder John tried to pick up living again, the more colorless and cold the world seemed and nothing felt the same. His psychosomatic limp was back and so was his PTSD eating disorder, although John didn't suffer from post-traumatic stress syndrome as bad as some soldiers, it did not completely pass him by and after he was released from the RAMC he developed a depression linked eating disorder that was common among PTSD sufferers. John knew they had crept up on him again but he just didn't have the strength or will to fight them and they came back to him like old familiar friends.

He remembered the night when Mycroft came to see him about the possibility of a new flat mate. Mycroft paced the small sitting room, his face shadowed with worry he as tried to talk to him and John sat, and nodded blankly while pretending to be listening.

John wasn't the only one that had changed for the worse since Sherlock's death and they both knew an end was coming soon. But the guilt of the elder Holmes made him more determined to never see that end happen, while the guilt of the soul shattered doctor silently longed for it.

The last thing Mycroft Holmes wanted to do was bury John next to his brother, no one's little brother should die before him and he knew he could not leave John to the same fate and to watch him give up and stop. Sherlock cheated, and they were the ones that had to stay behind to suffer in silence and play by the rules.

The next day Mycroft submitted the advertisement and told John he would interview the applicants and send the one he approved. He told John to behave himself and to at least try, if not for himself then for Sherlock. John calmly replied that Sherlock didn't try for him so why would he care, he was _dead,_ then John rose and left Mycroft behind in his office with his head in his hands and the burden of the casualties that his brother left behind.

John folded the paper and shut his eyes, giving into the nagging feeling of betrayal, of Sherlock and what they used to have as flat mates, but something inside him knew that maybe Mycroft was right, maybe having another body around would help him even for few more days to keep on. Even just for a little while before that would eventually fail like everything else did. John just wasn't sure if he wanted to keep on, he just didn't want to surrender and admit it out loud to himself or to Mycroft.

A knock on the door interrupted him and his internal battle. Sighing and taking a deep breath, he opened his eyes and silently hoped that it was the postman. He went and opened the door to the most unusual looking man John had ever seen. The man had his back turned to John, with his head tilted back and he was gazing up at the sky and was letting the rain fall softly upon him, his arms were raised as if receiving a present, as if the rain was one of the best gifts he had gotten in a long time.

"Yes?" John asked gruffly, annoyed about being intruded on and that he could do nothing to stop it as Mycroft's words echoed in his mind. The man whirled around with an ungraceful air and he stared at John for a few minutes, like John was someone he had heard about and this was the first time to meet him. John noticed the man's eyes were bright, but they also had a bit of sadness around the edges, like the look you see in an older person who has felt the heavy hand of time. "Hello, John Watson..." the man spoke softly, his voice trailed off and he began to look John over slowly, then he smiled softly and a bit sadly, as if John reminded him of a bittersweet memory, and he had come back to check to see if it was still where he had left it.

He suddenly shook his head as if he seemed to remember the reason why he had come, and with an excited "_Oh yes!"_ He dug like a little boy into his pocket of his coat, the touch of sadness around him now vanished and John thought he had imagined it as the trick of the light as the man pulled out a rumpled looking piece of paper from his pocket and with a flourish showed it to John, "I'm here about this, your advertisement for a flat mate, I have been approved by a My... Mycroft Holmes? is that it? Yes, well _him,_ I have been approved by him and here I am."

He fell silent for moment as if his speech blew over too quickly and he didn't know what else to do and John just stared at him as he looked back at John with calm expectancy, then looked quietly down at his shoes and waited for John to say something. Silently John took the piece of paper, nodding as he looked at it, he replied cold and stiffly, still rather unsure and skeptical of the man that stood before him like a happy stray dog who decided he had found a new home. "Yes, this is… mine, I mean, yes, it's for me."

"Good!" The man looked up, his eyes shining and clasped his hands together in glee as he smiled at John. "Well then, hello, John Watson. My name is The Doctor and I'm your new flat mate." As John opened his mouth to say something along the lines of "I don't need you or want you, and it will just be a waste of time so just go away and leave me alone." The man- The _Doctor - _turned back to gaze wistfully up at the sky like he had forgotten something up there.

"Nothing like a good September rain." He stated in a bit of a sad way and after turning and flashing John another smile, he waltzed past him into the flat. John heard his voice, filled with almost childish excitement, float back to him from the living room. "This is perfect! Bit grayish but I like the color gray, it has a feeling that no other color can offer, it's like rain.. I like rain, rain is good..."

John looked warily up at the nothing special to him gray clouds and sighed, as he folded the paper into his pocket, he turned and followed to see what he had just gotten himself into and the strange man he already resented and very deeply hoped would not stay long. John wondered if pretending to be alive would actually turn out to hurt worse than to accept that he was dead. And John didn't think that this unwelcome, strange-looking, lanky man with a crooked bow tie and a crumpled piece of paper would change a single thing.

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_A/N: Well, I hope you liked the beginning of my little Wholock drabble. I always enjoy your reviews and ideas._

_Reviewers get to hug the Doctor and help him unpack =)_

_Let me know your thoughts and hopes about it and if you are interested in seeing what happens to our dear Doctors as they try to figure how to try to live with each other and themselves._


	2. Chicken Soup For The Troubled Soul

_A/N: Here goes the second chapter, hope you enjoy it. Thank you to everyone who_ _has reviewed and followed so far._

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"So this is your room," John said as he let the door slide open. The Doctor hesitated outside of the doorway as he leaned over and peered a bit timidly inside. "My room," he softly repeated John's words, then he took a step inside and began slowly turning around, gazing as if it had been a long time since he had been in or had a room like this before. He began to touch the furniture, he ran his hand along the bed and he patted it gently with his slender hand as if it were an old friend, then he looked up and smiled brightly at John, "My room, it's perfect."

Before John could answer, the Doctor uttered a delighted squeak and threw himself face down on the floor and wriggled under the bed, all John could see of him was his skinny legs and his green striped socks showing between his pant leg and shoes as they stuck out from under the bed. "Hello!" John heard the muffled exclamation come from under the bed "Look at all this room! you can keep all sorts of interesting things under here." The legs waved in excitement.

"It's just a room," John replied gruffly, "Nothing special about it, it's not even decorated." The other mans pleasure at something so simple had made him slightly angry.

"Yes, but… it's my room," The doctor replied, not phased in the least by John's gruffness as he wriggled out from underneath the bed and brushed off the adorning dust bunnies. "That is what makes it special." he added, as he started imagining all the things could do to decorate it.

"Would you help me?"

"What?" John asked with a quiet sigh, slightly unsure of what was coming.

"Will you help me decorate my room, I never decorated one before." John looked at the man kneeling on the floor, looking up at him in hopeful expectation.

"Me? No, I mean it's not my room. Just decorate it however you want, whatever you do will be fine." He tried to ignore the disappointment that filled the Doctor's face as he looked down at the dust bunny he was carefully holding and softly said, "Oh, alright then, thank you, John Watson."

John tried to ignore the prick of his conscious, he could see that the Doctor knew John didn't like him, and it made John all the more frustrated that the Doctor was pretending not to notice and acting like John was treating him like his best friend, _I have no friends._ John mentally slapped himself and called over his shoulder as he left the room, "Good, come on then, there's some food in the kitchen if you're hungry."

The Doctor's face lighted up, the disappointment from John's brush off now hidden "I am rather hungry." The Doctor admitted as he slipped the dust bunny into his pocket and gave his room a little farewell wave as he rose to follow John down the stairs, _well_ tripped down them actually, John had not seen someone so graceful and yet so clumsy since Sherlock.

John looked the around the small kitchen for something to eat deciding that this would be the only time he would make something for the man, after this he was on his own, John knew that he would have to go shopping soon as he realized that he had nothing besides a container of custard, a can of rather plain chicken soup and a box of fish fingers.

Never being in the mood to eat much of anything, he never took much care in what food he had. Mrs. Hudson brought him things sometimes but other than that, he couldn't remember the last time he went food shopping.

"Do you like chicken soup?" John asked over his shoulder as he went to the fridge. The Doctor hesitated for a moment as if he was thinking and then cheerfully replied, "I don't know… I don't remember ever having a chicken soup." He floated over and sat down at the kitchen table, he folded his hands together and he watched John excitedly as if he was going to do a magic trick.

"Oh, okay then," John replied, frowning slightly,_ how does someone not know about chicken soup? Everyone has eaten chicken soup at least once in their life, but I suppose normal would not be something to label him, even Sherlock, no do not think of Sherlock, he is nothing like Sherlock. _John shook his head to clear his thoughts and sighed, the new flat mate had only been here for an hour and was already testing John's patience.

"Lets try the soup then, it's really good," replied John. As calmly as he could as he opened the can, then after heating some up under the watchful gaze of the Doctor, it seemed like the man was studying every move he made as if he was learning. John set a spoon and a bowl of the soup before him, the doctor excitedly picked up the spoon and took a bite, held it in his mouth for a second, and then immediately made a face and ungracefully let the mouthful of soup fall back into his bowl, he wiped at his tongue and mouth with his fingers and he grimaced as he looked up at the shocked John sitting at the table across from him.

Before John could move or say a word, the Doctor walked over and threw his soup –bowl and all- out of the open kitchen window and as he wiped his hands on his coat with a satisfied air he yelled after the shattering of the bowl, "And don't come back!" And as an after thought he added "Ya nasty!"

He started calmly muttering to himself as he shut the window "Chicken soup, nasty stuff, just chicken sweat with faux bits in it, can't risk that trying to crawl back in here." John found himself pulling his own soup bowl protectively towards him as the doctor-_madman _turned and warily looked at him and his soup bowl.

John tried to snap himself out of the shock of what just happened, he closed his mouth and tried to swallow his anger that was trying to get the best of him as he stammered "I have a box of frozen fish fingers and some custard a friend of mine made for me, how… how would that be?"

He was surprised by how well he was taking what had just happened with the soup incident but he guessed it was all the years he had spent with Sherlock. After life with Sherlock, nothing could really surprise him now and he had agreed to Mycroft that he would behave himself, that meant not kicking the man out the first day even if he did break his dishes and trip over his own feet for the third time that morning.

The Doctor was silent for a moment. He straightened his crooked bow tie as if composing himself from the chicken soup ordeal and nodded as he looked away from John, "I… I would like that, I have not had them in a very... long time," His voice had a far away sadness to it as he walked back to his seat at the table.

"Alright then," John replied dumping out his soup himself, he didn't want to lose another bowl to a casualty and started pulling out the items from the fridge. He heated up the fish fingers and dished out the custard that Mrs. Hudson had brought him. "We will stay away from chicken soup, I wasn't aware of how lethal it would be." His voiced was tinged with sarcasm.

"Yes," the doctor replied gravely, "A bit not good, that." John froze as he heard Sherlock's voice in his mind_, "A bit not good John? a bit not good."_ John slammed the cupboard door, startling the Doctor behind him who was examining the salt and pepper shakers.

_Stop it, John, he is not Sherlock and you can't let him haunt you with his memory._

As he set the food down on the table, John said "We can go shopping tomorrow I suppose, as I'm sure you have things that you need to get," The Doctor nodded as he slowly pulled his plate closer to him. He stared down at his fish and custard, and John was shocked to see that the Doctor looked like he was going to cry, he was sure he could see tears in the smaller man's eyes. "Do fish fingers and custard always make you cry?" He asked, his eyebrows raised in question at the strange oddities of his new flat mate.

The Doctor looked up him, he was indeed a bit misty eyed, and smiled sadly at him, "They… they didn't used to," he whispered as he picked up one of the fish fingers and delicately dipped it into his custard. He made a gesture with it as if saluting some memory, then he smiled at John and began eating as if he didn't have a care in the world, in which John was beginning to suspect was somewhat of a lie, he could tell the motions of someone faking the truth, he was an expert at it.

John groaned silently _what did he care,_ he dreaded the thought of all the meal times to come in the future and how he was going to survive them and this new flat mate, who already reminded him of someone he used to know.

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_A/N: Reviewers get to help pick the kinds of food the Doctors buy on their shopping trip_ _expedition._


	3. Doctors In Hospital Beds

After they had finally finished eating, much to John's relief, the Doctor begged to help with the dishes, and so for a few minutes the air was filled with the happy chatter of the Doctor as he dried and the flapping flurry of the dish towel mixed with the occasional grunts from John who was washing and trying to ignore him.

They almost made it through all the dishes without casualty until the Doctor finally dropped a soup bowl and it crashed to the floor. _The last of its kind, _John thought in dismay as both Doctors stared forlornly down at the sad and shattered remains of the loyal soup bowl.

The Doctor tried to clean the mess up but was immediately kicked out of the kitchen by John in a way the Doctor could only describe as "Raging" and he wandered sadly into the living room after surrendering his dish towel.

After finally getting the shattered pieces swept up and finishing the rest of the kitchen, John realized he had not heard any noise from the Doctor for the last fifteen minutes or so.

Worried at what else he might find damaged beyond repair, he went and looked for his new erratic flatmate, dreading that he might actually find him and to his disappointment he did find him. Sprawled upside down on the settee and watching the telly.

His ankles were crossed and they were resting against the wall, his head dangling a few inches off the floor as it hung off the settee and he was clutching the union jack pillow in his arms as he crowed with happiness at a _Monty Python_ sketch.

"Hello!" He cheerfully greeted John from his upside down position, "Want to come watch? It's the _Gangster Granny_ sketch, I think you'd like it, you have to watch out for grannies, you know. They can turn on you in a flash."

John shook his head, clenching his left hand, trying to hide his frustration he knew had no reason to be there. "I'm going to bed, don't forget to turn off the telly when you're done."

The Doctor plopped ungracefully over onto his side on the settee cushions and looked at John sadly as he tried to untangle his arms and legs from each other, trying not to fall completely off the settee and onto his head.

"Oh, alright then," He replied as he stood up in triumph over his battle with his uncooperative limbs and he followed John down the hall to his bedroom chattering about what they would get when they went shopping.

"I haven't been shopping in a shop for ages," The Doctor said excitedly, "Do you think they will have any jammy dodgers? Are they still the sa-" They had reached John's room and he almost ran into John, who turned around angrily, stopping him abruptly in his rambling.

"Look," John said gruffly, "I don't care what you get, just buy whatever you like, as long as I don't have to hear about it." And he shut his door in the Doctor's face, leaving him alone in the hallway.

The Doctor stood outside the door for a few minutes, his head bowed as he looked down at his shoes, realizing that he was so very tired and that John was not coming out again. After turning off the telly and switching off the living room lamp, the Doctor headed upstairs to his room, too tired to even be glad about spending his first night in his real room.

The Doctor sat down on the edge of his bed, glad for the sound of silence that filled the room but hating how it made him miss the soft, warm hum of the TARDIS.

He heard the soft pattering of the rain against the window pane and thought about the TARDIS, alone in the rain. He had placed her in a safe spot, and Mycroft Holmes had promised that he would keep an eye on her and that she would be quite safe where she was.

He then remembered the box of old books that was in the back of his closet. John had said they were just old copies that he didn't want any more but didn't want to throw away.

The Doctor couldn't remember the last time he even picked up a book and he jumped up excitedly from the bed, dived into his closet and pulled out the box with excited glee.

Kneeling before the box, he discovered that it contained several old dog-eared paperbacks, mostly old biographies and war stories. Old news, been there, done that type of read.

But one title caught his eye, _Tuck Everlasting._ He picked it up and nearly gasped as somewhere in the back of his mind he recognized it. "Oh, look Amy!" He exclaimed cheerfully as he gently stroked the book.

"This is your favorite book remember? You read it all the time in the TARDIS and you always said it was a favorite of yours from when you were little, you even said you would read it out loud to me one day, remember, Amy?"

He looked up from the book and his eyes searched his room, expecting to meet the sassy hazel eyes that he knew so well. Only silence answered him and he took a deep breath as he caught himself.

"Oh…" He said in a disappointed whisper as he looked around his empty room and his smile faded as he realized where he was and that he was alone. Amy wasn't there beside him; he had just been talking to himself again.

He looked down at the book in his hands and his eyes blurred with bitter tears as he unwillingly remembered that Amy was gone and in her place, just like the others, was left the ever present countdown of empty years since he had lost her. Five years eight months and twenty-four days gone. But it felt like a thousand.

"Not just Amy." He whispered shakily, as a tear fell onto the worn out cover of the book. All of them, _all _of them were gone now. His beautiful, amazing companions, so many wonderful beginnings and so many heart breaking endings. Except for him, he never got an ending and he was left alone, just him and the ghosts he once knew. He could see their faces and could feel their hands resting softly upon his bowed head as if to comfort him with their memory.

He slowly pushed all the books except _Tuck Everlasting_ back into the closet and went and laid back on his bed. As he clutched the book, he tried to tell himself that it was alright, he had just forgotten again.

He had been doing it a lot during the past few months, forgetting that he was alone and that they had faded away. His mind playing tricks on him, thinking that _they_ were there with him, laughing and talking beside him. The first time it happened, he had spent a whole day running around the TARDIS, chattering excitedly away to Donna Noble about a type of flying snail he had stumbled over one day.

He didn't even realize she wasn't actually there until he passed a mirror and saw only his own reflection dash by and no Donna behind him. He went back to the mirror and found only his own eyes staring back at him and as he whirled around and looked frantically for Donna, begging her to say something, he realized that the emptiness surrounding him had been real, and his Donna _was not_ real. It was just himself.

It had disturbed him so much, that all he could do was to sit on the TARDIS floor and stare at his reflection.

As he sat there, he tried to sort his memories and put them where they belonged, trying to keep the past separate from the present, but they kept slipping away from him, unwilling to stay in their proper places, unwilling to accept the truth.

After a while, he finally stopped trying, as the faces and voices of the past overcame him, reminding him that _he_ was the memory and the one that got left behind while the others had to go on living. Too exhausted to fight his mind and memories, he just gave in and hugging his knees to his chest he cried hopelessly for himself and his overwhelming reality while the TARDIS silently watched over him.

As he lay there on the bed he thought about John Watson, the man pretending to be asleep downstairs and the promise he had made to stay and look after him during Sherlock's absence.

The Doctor had been grateful to have a chance to slow down and try something new. He had always dreaded living in a house and doing normal things that normal people did, but as the years darkened, and the companions kept leaving, he thought it might not be so bad to give it a try after all.

He would miss the traveling, but somehow he knew that he desperately needed this, and so did the TARDIS. He had realized he wasn't who he used to be and that this was his chance to slow down and rebuild himself. The man who carried the weight of the universe was terribly tired, both physically and mentally and needed to rest his world wearied shoes.

They always said the best road to recovery was to help someone else.

He laughed, a bit sadly, to himself, "I wonder, will I be able to help someone else when I can't even save myself? I'm just a tired old man," He whispered as he stared up at the starless ceiling, "Lying on a bed and losing my mind. I can save planets and galaxies, but myself? I have nothing left for myself."

He lay there, listening to the rain falling and the night hours silently pass. The dark clouds rolled over him and they seeped through the cracks in his mind.

_Some medicine I am, one broken doctor coming to try to help another broken doctor, this must be where the broken and used up doctors go to die. They can't help each other and they can't help themselves so they just lay here in their pretend hospital beds until they lose their minds from the reality of things they have lost and their hearts stop from lifeless apathy_…

The text tone of his mobile startled him out of his thoughts, no one had texted him in a very long time but he remembered who it would be, especially at this time of night.

**Blocked Number: How is he?**

**TD: Just like you said and he also dislikes me very much.**

**Blocked Number: Give him time, he'll come around.**

**TD: How can you be so sure?**

**Blocked Number: Because, I know him and I know you, don't worry, he'll come around, He reminds me of you, when we first met.  
**

**TD: I suppose he does. Thanks for the jelly babies, by the way. I didn't think you remembered. It's been ages since I've had a good jelly baby.**

**Blocked Number: You're welcome, and I always remember.**

**Thank you for doing this, Doctor, you are the only one that can, and I have always trusted you. I have to go now, it won't be long now and I'll see both of you again soon.  
**

"Take care of yourself, Sherlock." The Doctor softly said as he deleted the messages from his phone. Well, even if he didn't believe in himself to keep his promise and help John Watson, he knew Sherlock did and maybe, that was all he needed.

Who knew, maybe as he lay in his hospital bed, trying to find and repair his own shattered remains, he might enjoy himself. It wasn't everyday that he had the opportunity to live in a flat and do what people who lived in flats do; it might even be fun at that.

"Of all the things I've lost, I miss my mind the most." He laughed as he wiped at his eyes, erasing the effect of the tears that Sherlock's trust had brought on him.

Turning off his bedroom light, he pulled his covers over his head. He switched on the torch he had brought with him. In the safety of his cover fortress, he opened _Tuck Everlasting _and as he began to read, it was Amy's voice reading to him that faded the sound of rain and the fear and uncertainty of what lay ahead.

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_Reviewers get a bag of jelly babies._

_Thanks for reading! the next chapter will be **The** **Dreaded Shopping Trip**... poor John =)_

_Any suggestions for foods the Doctors should get?_


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